Breast Cancer Relapse-free Survival Research Articles

Endosomal protein expression of γ1-adaptin is associated with tumor growth activity and relapse-free survival in breast cancer.

γ1-Adaptin is a subunit of adaptor protein complex-1 (AP-1), which regulates intracellular transport between the trans-Golgi network (TGN) and endosomes. Since expression levels of AP-1 subunits have been reported to be associated with cell proliferation and cancer malignancy, we investigated the relationships between the immunohistochemical expression of γ1-adaptin and both clinicopathological factors and relapse-free survival (RFS) in breast cancer tissue. SK-BR-3 cell line depleted of γ1-adaptin was used for cell proliferation, migration, and invasion assay. Intracellular localization of γ1-adaptin was examined with immunohistochemistry (IHC) using an antibody against γ1-adaptin, and with double immunohistofluorescence (IHF) microscopy using markers for the TGN and endosome. γ1-Adaptin intensities in IHC samples from 199 primary breast cancer patients were quantified and assessed in relation to clinicopathological factors and RFS. Cell growth, migration, and invasion of SK-BR-3 cells were significantly suppressed by the depletion of γ1-adaptin. Although the staining patterns in the cancer tissues varied among cases by IHC, double IHF demonstrated that γ1-adaptin was mainly localized in EEA1-positive endosomes, but not in the TGN. γ1-Adaptin intensity was significantly higher in the tumor regions than in non-tumor regions. It was also higher in patients with Ki-67 (high), ER (-), PgR (-), and HER2 (+). Among subtypes of breast cancer, γ1-adaptin intensity was higher in HER2 than in luminal A or luminal B. The results of the survival analysis indicated that high γ1-adaptin intensity was significantly associated with worse RFS, and this association was also observed in group with ER (+), PgR (+), HER2 (-), Ki-67 (high), or luminal B. In addition, the Cox proportional hazards model showed that high γ1-adaptin intensity was an independent prognostic factor. These results suggest that the endosomal expression of γ1-adaptin is positively correlated with breast cancer malignancy and could be a novel prognostic marker.

Clinical biostatistics in the 2020s

Clinical biostatistics in the 2020s

Genetic co-expression networks contribute to creating predictive model and exploring novel biomarkers for the prognosis of breast cancer

Genetic co-expression network (GCN) analysis augments the understanding of breast cancer (BC). We aimed to propose GCN-based modeling for BC relapse-free survival (RFS) prediction and to discover novel biomarkers. We used GCN and Cox proportional hazard regression to create various prediction models using mRNA microarray of 920 tumors and conduct external validation using independent data of 1056 tumors. GCNs of 34 identified candidate genes were plotted in various sizes. Compared to the reference model, the genetic predictors selected from bigger GCNs composed better prediction models. The prediction accuracy and AUC of 3 ~ 15-year RFS are 71.0–81.4% and 74.6–78% respectively (rfm, ACC 63.2–65.5%, AUC 61.9–74.9%). The hazard ratios of risk scores of developing relapse ranged from 1.89 ~ 3.32 (p < 10–8) over all models under the control of the node status. External validation showed the consistent finding. We found top 12 co-expressed genes are relative new or novel biomarkers that have not been explored in BC prognosis or other cancers until this decade. GCN-based modeling creates better prediction models and facilitates novel genes exploration on BC prognosis.

Association of Circulating Tumor DNA With Disease-Free Survival in Breast Cancer

Fragmented DNA is continuously released into the circulation following apoptosis and necrosis of both cancerous and noncancerous cells; when it is released by cancer cells, it is specifically known as circulating tumor DNA (ctDNA). Previous studies have suggested that ctDNA can reflect tumor burden and guide potential therapeutic targets. To determine the association of ctDNA with breast cancer disease-free survival (DFS) and progression-free survival in early, locally advanced, and metastatic breast cancer. An electronic search was conducted using the Cochrane Library, ScienceDirect, PubMed, and Embase from July 30, 2019, to October 31, 2019; all languages were included. The following search terms were used: ctDNA OR circulating tumor DNA OR liquid biopsy AND breast cancer OR breast carcinoma OR breast tumor AND prognosis OR survival. All titles were screened, and the appropriate abstracts were reviewed. If any data were missing, the authors contacted the study authors for permission to access data and extrapolate hazard ratios (HRs). To be included in the analysis, the studies had to meet the following prespecified inclusion criteria: (1) a ctDNA blood sample was measured; (2) DFS, progression-free survival, or relapse-free survival was reported as an HR; and (3) the patient population only had breast cancer. Retrospective and prospective observational cohort studies were included. Two authors (C.C. and C.F.) independently reviewed the literature. All data were recorded independently by both authors and were compared at the end of the reviewing process to limit selection bias. Duplicates were removed and any disparities were clarified. Data were pooled using a fixed-effects or random-effects model according to the study heterogeneity. This study adhered to the guidelines of the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) and Meta-Analysis of Observational Studies in Epidemiology (MOOSE). The primary outcome was the association of ctDNA with DFS or relapse-free survival in breast cancer. Secondary outcomes focused on subgroup analysis in the setting of early breast cancer and metastatic breast cancer. From a total of 263 publications found using the predefined search terms, data from 8 studies (3.0%) reporting on 739 patients in total were suitable for inclusion. Circulating tumor DNA gene variation detection (both before and after treatment) was statistically significantly associated with shorter DFS (HR, 4.44; 95% CI, 2.29-8.61; P < .001). Detection of ctDNA was statistically significantly associated with a reduction in DFS in both the early breast cancer subgroup (HR, 8.32; 95% CI, 3.01-22.99; P < .001) and the metastatic or locally advanced subgroup (HR, 1.91; 95% CI, 1.35-2.71; P < .001). Pretreatment and posttreatment plasma sample collection was analyzed in both early and metastatic groups. The posttreatment group encompassed both surgical and oncologic therapy. Pretreatment plasma detection of ctDNA was statistically significantly associated with reduced DFS (HR, 3.30; 95% CI, 1.98-5.52; P < .001). Posttreatment sampling of ctDNA failed to achieve statistical significance (HR, 8.17; 95% CI, 1.01-65.89; P = .05). In this systematic review and meta-analysis, elevated plasma ctDNA was associated with a high risk of relapse. This finding suggests that plasma ctDNA may provide an excellent method to stratify risk and personalize patient follow-up.

Systemic Analysis of the Prognosis-Associated Alternative Polyadenylation Events in Breast Cancer.

Alternative polyadenylation (APA) is a post-translational modification that occurs during mRNA maturation in humans. Studies suggested that abnormal APA events are associated with the genesis and progression of malignant tumors. Here, we aimed to comprehensively evaluate the prognostic value of APA events involved in breast cancer (BC). Both APA events and clinical information for BC patients were downloaded from The Cancer Genome Atlas (TCGA) database to identify prognosis-related APA events in BC. A total of 462 APA events and 374 APA events were shown to be significantly related to overall survival (OS) and relapse-free survival (RFS), respectively, of BC patients. The TCGA set was randomly divided into a training and a test set. Key prognosis-related APA events were selected by LASSO regression to build prediction signatures for OS and RFS by multivariate Cox regression analysis in the training, test, and whole set. BC patients were stratified into high-risk and low-risk groups based on median risk scores. Kaplan–Meier survival analysis demonstrated that low-risk groups had better OS and RFS than high-risk groups in all three sets. The time-dependent receiver operating characteristic (ROC) curves showed that our signatures had a good predictive ability for survival and recurrence for BC patients in all three sets. The independent prognostic indicators-based nomogram model had excellent performance and considerable net benefit for predicting the OS and RFS in BC. A PPI network was constructed between key prognosis and core regulators associated with APA, consisting of 48 nodes and 244 edges. Functional enrichment analysis also revealed their association with RNA processing and RNA synthesis. Collectively, our data indicate that prognostic signatures based on APA events may be powerful prognostic predictors for OS and RFS in BC.

Experimental, Clinical, and Morphological Analysis of H-Ras Oncoproteins for Locally Advanced Breast Cancer

BACKGROUND: Activated forms of RAS increase both in breast cancer and in cell lines in the presence of estimated glomerular filtration rate (EGFR) or HER2 expression. HRAS oncoproteins play an important role in enhancing the proliferation and resistance of breast cancer tumor cells to apoptosis. A number of studies have shown a significant decrease in EGFR expression after neoadjuvant chemotherapy, which has been clinical, manifested by an improvement in immediate efficacy and an increase in overall and relapse-free breast cancer survival rates.&#x0D; AIM: The aim of the study was to study relapse-free survival depending on the expression of the H-RAS oncoprotein in patients with breast cancer who received different treatment regimens for the farnesyltransferase inhibitor.&#x0D; METHODS: H-RAS status was assessed by immunohistochemistry.&#x0D; RESULTS: A comparative analysis of patients with negative expression of H-RAS oncoproteins showed a statistically significant increase in relapse-free survival in the subgroups who received neoadjuvant chemotherapy according to the AC regimen (adriablastin + cyclophosphamide) and AC + arglabin, compared with monotherapy by arglabin: Kruskal–Wallis= 12.56, where p = 0.001. A comparative analysis of patients with positive expression of H-RAS showed that in the subgroups treated with arglabin and AC+arglabin, there was a statistically significant increase in relapse-free survival compared with the AC subgroup: Kruskal–Wallis = 10.96, where p = 0.004. It was established that the positive expression of H-RAS negatively affects not only the direct effectiveness of neoadjuvant therapy but also worsens the rates of relapse-free survival. However, in patients with positive H-RAS expression who received arglabin in monotherapy, there was a statistically significant increase in relapse-free survival up to 16.5 ± 1.1 months compared with the standard AC regimen (13.5 ± 1.1 months) (р ˂ 0.05), the addition of arglabin to the standard AC regime also increased this indicator to 16.4 ± 1.2 months (р ˂ 0.05).&#x0D; CONCLUSION: These results may indicate the clinical applicability of determining H-RAS as a prognostic factor for relapse-free survival in breast cancer.

8p11.23 Amplification in Breast Cancer: Molecular Characteristics, Prognosis and Targeted Therapy.

Background: Amplification of the locus 8p11.23 has been observed in cancer and genes of this locus, including ZNF703 (Zinc finger protein 703), NSD3 (Nuclear receptor binding SET domain protein 3) and FGFR1 (Fibroblast growth factor receptor 1), have been put forward as dominant oncogenes conferring pathophysiologic benefit in cancers with amplifications. However, there is no consensus on the importance of each of them or any other genes of the amplicon or even a consensus on which genes are part of the amplicon. Methods: Publicly available data were used to characterize the locus amplified at 8p11.23 and derive information on each of the genes and roles as oncogenes. The frequency of the amplifications in the locus was examined in the cBioportal platform, and expression levels of the amplicon genes in amplified cases were derived from genomic studies reported in the platform. Examination of the influence of mRNA expressions of each gene of the locus for Recurrence-free survival in breast cancer was performed using K-M plotter. Results: The 8p11.23 amplicon is present in higher frequency in squamous cell lung carcinomas, breast cancers and bladder carcinomas and is only rarely observed in other cancers. The most frequently amplified genes within the amplicon vary between different types of cancers. In breast cancer, amplified cases are most commonly of the luminal B type. Amplified genes are not always over-expressed and there is a low correlation of amplification with over-expression in amplicon genes with variation between genes. The presence of the amplicon does not influence the aneuploidy score or the tumor mutation burden of breast cancers. Regarding prognosis, the two genes of the amplicon whose mRNA hyper-expression portends adverse relapse-free survival in breast cancer are EIF4EBP1 (Eukaryotic transcription initiation factor 4E binding protein 1) and LSM1 (LSM1 homolog, mRNA degradation associated). Conclusion: Besides the previously proposed genes to play a role as dominant oncogenes in the 8p11.23 cancer amplified locus, other genes may also be important in breast cancer based on the high correlation of their amplification and mRNA expression and adverse prognosis conferred by over-expression, consistent with an oncogenic role.

Comprehensive Analysis of Fibroblast Growth Factor Receptor (FGFR) Family Genes in Breast Cancer by Integrating Online Databases and Bioinformatics.

BackgroundFibroblast growth factor receptors (FGFRs) play vital roles in the development and progression of human cancers. This study aimed to comprehensively understand the prognostic performances of FGFR1–4 expression in breast cancer (BC) by mining databases.Material/MethodsThe levels of FGFR1–4 expression in BC were analyzed by online databases, GEPIA (Gene Expression Profiling Interactive Analysis) and UALCAN. Survival analysis of FGFR1–4 was carried out by Kaplan-Meier plotter. GSE74146 was downloaded from Gene Expression Omnibus (GEO) and analyzed by GEO2R to screen the differentially expressed genes (DEGs) between FGFR2-silenced BC cells and control. Over-presentation for DEGs were done by Enrichr tool. Networks of DEGs were obtained by using Search Tool for the Retrieval of Interacting Genes (STRING) and Cytoscape software. Hub genes were identified by cytoHubba Cytoscape plugin.ResultsThe online databases showed that FGFR1 was significantly downregulated whereas FGFR3 was upregulated in BC. Kaplan-Meier plotter demonstrated the upregulation of both FGFR1 and FGFR3 indicated favorable relapse free survival (RFS) whereas FGFR4 overexpression predicted unfavorable overall survival (OS) in BC patients. Importantly, our results showed FGFR2 overexpression robustly predicted favorable OS and RFS in BC. Further bioinformatics analysis of GSE74146 suggested FGFR2 mainly participated in regulating degradation and organization of the extracellular matrix and signaling of retinoic acid. Moreover, CXCL8, CD44, MMP9, and BMP7 were identified as crucial FGFR2-related hub genes.ConclusionsOur study comprehensively analyzed the prognostic values of FGFR1–4 expression in BC and proposed FGFR2 might serve as a promising biomarker. However, the underlying mechanisms remain to be elucidated.

Abstract OT1-02-02: A pilot study to examine the feasibility of measuring CTC and inflammatory biomarker changes resulting from atorvastatin as adjuvant therapy in TNBC and TN-IBC patients with residual disease after neoadjuvant chemotherapy

Abstract Background: Patients who have TNBC or triple negative-IBC (TN-IBC) and do not achieve pathological complete response after neoadjuvant chemotherapy are at significant risk for distant relapse and death from recurrent disease. Apart from capecitabine, there are no proven adjuvant therapies that may improve these poor outcomes of patients with chemo-resistant tumors. Therefore, there is an unmet need for effective systemic therapy for this subset of patients with TNBC. Epidemiological evidence reveals that statin use after diagnosis is associated with improved breast cancer relapse-free survival and decreased mortality. However, direct evidence of in vivo mechanisms explaining this association are lacking. Preclinical studies using statins in breast cancer reveal pathways that statins can inhibit proliferation, stem cell self-renewal and metastatic potential. Trial Design: This is a pilot study designed in 2 phases to assess feasibility of completion while providing a signal of efficacy in biomarker changes. In the first phase, we will follow the initial 30 patients who meet eligibility for atorvastatin treatment for the 2-year treatment window, or until disease recurrence. We will collect blood samples prior to, and during atorvastatin treatment for circulating tumor cells (CTCs), cytokine and inflammatory biomarker analyses. We defined a positive outcome as CTCs remaining non-detected at 6 months when baseline CTC is undetected, or a reduction in the number of CTCs at 6 months compared to baseline. If we observe a positive outcome among the initial 30 patients, then we will open the second phase of this study for an additional 50 patients. Here we will follow both patient cohorts who receive and not receive atorvastatin treatment to collect longitudinal data on biomarkers as a function of the natural history of TNBC to better understand the activity of atorvastatin. Trial Eligibility: Patients with stage II-III TNBC who have residual cancer burden (RCB)-II or RCB-III or stage 3 TN-IBC with any amount of residual disease, and are not taking a statin or any other anti-lipidemic agent are candidates for the study. Patients must have adequate hematologic, organ, and cardiac function and must have recovered from the acute effects of any prior treatments. Baseline lipid profile will be assessed by a cardiologist to determine the patients’ eligibility to take atorvastatin based on current ACC/AHA guideline, and to select between moderate (20mg) or high intensity treatment (40mg). Specific Aims: The primary objective is to determine the proportion of patients with undetectable CTCs at 6 months with and without atorvastatin therapy. Secondary objectives include correlation of baseline lipid profiles/lipid profile changes with 2 year-relapse free survival (RFS), CTC counts and inflammatory biomarkers. Statistical Methods: The total estimated enrollment is 80 patients, including at least 5 treated with adjuvant capecitabine and at least 5 without adjuvant capecitabine. The study overall is powered with the assumption that 48 patients will receive atorvastatin and 32 will not, and this will allow us to estimate the percent of patients with negative CTCs at 6 months with a standard error not larger than 7% and 9%, respectively. All other analyses including inflammatory biomarkers and RFS differences between groups are exploratory and considered hypothesis-generating rather than conclusive. Citation Format: Angela Alexander, Takeo Fujii, Michael C Stauder, Wendy A Woodward, James M Reuben, Yu Shen, Diane Liu, Sangeetha M Reddy, Vicente Valero, Susan C Gilchrist, Bora Lim, Anthony Lucci, Naoto T Ueno, Carlos H Barcenas. A pilot study to examine the feasibility of measuring CTC and inflammatory biomarker changes resulting from atorvastatin as adjuvant therapy in TNBC and TN-IBC patients with residual disease after neoadjuvant chemotherapy [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr OT1-02-02.

Tailored dose-dense chemotherapy in combination with trastuzumab as adjuvant therapy for HER2-positive breast cancer: A secondary analysis of the phase III PANTHER trial.

553 Background: Dose-dense (DD) adjuvant chemotherapy improves outcomes in early breast cancer (BC). However, there are no data to inform on the combination of DD chemotherapy with trastuzumab for patients with HER2-positive disease. Methods: This is a protocol predefined secondary analysis of the randomized phase 3 PANTER trial. Women 65 years old or younger with node-positive or high-risk node negative BC were randomized 1:1 to either tailored according to hematologic nadirs and DD epirubicin/cyclophosphamide (4 cycles) followed by 4 cycles of docetaxel (tDD EC/D) or standard 3-weekly 5-fluorouracil/E/C (3 cycles) and D (3 cycles); Patients with HER2-positive disease received 1 year of adjuvant trastuzumab. In addition, HER2-positive and an equal number of matched for age, treatment group and institution, HER2-negative patients that were enrolled in Swedish sites were enrolled in a predefined study of cardiac safety and underwent echocardiography or MUGA and electrocardiography at baseline and at four and six years of follow-up. The primary endpoint was BC relapse-free survival (BCRFS). Results: There were 342 HER2-positive patients; 335 received at least one dose of trastuzumab, while 29 patients discontinued trastuzumab prematurely. BCRFS was not statistically significantly in favor of tDD EC/D (HR = 0.68, 95% CI 0.37 – 1.27, P= 0.231). Cardiac outcomes after four and six years of follow-up did not differ significantly between HER2-positive and HER2-negative patients, nor between tDD and standard treatment. Conclusions: To our knowledge, these are the only data on combining DD adjuvant chemotherapy and trastuzumab in BC. The combination decreased the risk for BC relapse by 32% compared to standard treatment, a statistically non-significant difference. Its efficacy and safety merit further evaluation as part of both escalation and de-escalation strategies. Clinical trial information: NCT00798070.

Identification of novel GLI1 target genes and regulatory circuits in human cancer cells.

Hedgehog (HH) signaling is involved in many physiological processes, and pathway deregulation can result in a wide range of malignancies. Glioma‐associated oncogene 1 (GLI1) is a transcription factor and a terminal effector of the HH cascade. Despite its crucial role in tumorigenesis, our understanding of the GLI1 cellular targets is quite limited. In this study, we identified multiple new GLI1 target genes using a combination of different genomic surveys and then subjected them to in‐depth validation in human cancer cell lines. We were able to validate >90% of the new targets, which were enriched in functions involved in neurogenesis and regulation of transcription, in at least one type of follow‐up experiment. Strikingly, we found that RNA editing of GLI1 can modulate effects on the targets. Furthermore, one of the top targets, FOXS1, a gene encoding a transcription factor previously implicated in nervous system development, was shown to act in a negative feedback loop limiting the cellular effects of GLI1 in medulloblastoma and rhabdomyosarcoma cells. Moreover, FOXS1 is both highly expressed and positively correlated with GLI1 in medulloblastoma samples of the Sonic HH subgroup, further arguing for the existence of FOXS1/GLI1 interplay in human tumors. Consistently, high FOXS1 expression predicts longer relapse‐free survival in breast cancer. Overall, our findings open multiple new avenues in HH signaling pathway research and have potential for translational implications.

Notch3 Maintains Luminal Phenotype and Suppresses Tumorigenesis and Metastasis of Breast Cancer via Trans-Activating Estrogen Receptor-α.

The luminal A phenotype is the most common breast cancer subtype and is characterized by estrogen receptor α expression (ERα). Identification of the key regulator that governs the luminal phenotype of breast cancer will clarify the pathogenic mechanism and provide novel therapeutic strategies for this subtype of cancer. ERα signaling pathway sustains the epithelial phenotype and inhibits the epithelial-mesenchymal transition (EMT) of breast cancer. In this study, we demonstrate that Notch3 positively associates with ERα in both breast cancer cell lines and human breast cancer tissues. We found that overexpression of Notch3 intra-cellular domain, a Notch3 active form (N3ICD), in ERα negative breast cancer cells re-activated ERα, while knock-down of Notch3 reduced ERα transcript and proteins, with alteration of down-stream genes, suggesting its ability to regulate ERα. Mechanistically, our results show that Notch3 specifically binds to the CSL binding element of the ERα promoter and activates ERα expression. Moreover, Notch3 suppressed EMT, while suppression of Notch3 promoted EMT in cellular assay. Overexpressing N3ICD in triple-negative breast cancer suppressed tumorigenesis and metastasis in vivo. Conversely, depletion of Notch3 in luminal breast cancer promoted metastasis in vivo. Furthermore, Notch3 transcripts were significantly associated with prolonged relapse-free survival in breast cancer, in particular in ERα positive breast cancer patients. Our observations demonstrate that Notch3 governs the luminal phenotype via trans-activating ERα expression in breast cancer. These findings delineate the role of a Notch3/ERα axis in maintaining the luminal phenotype and inhibiting tumorigenesis and metastasis in breast cancer, providing a novel strategy to re-sensitize ERα negative or low-expressing breast cancers to hormone therapy.

PANTHER: Prospective randomized phase III trial of tailored and dose-dense versus standard tri-weekly adjuvant chemotherapy for high-risk breast cancer in the modern era of endocrine and anti-HER2 therapy.

1002Background: Standard dosing of chemotherapy (ct) based on body surface area results in marked inter-patient variation in pharmacokinetics, toxicities and efficacy. Methods: 2,017 patients with node-positive or high-risk node-negative breast cancer were randomized (1:1) in 86 centers in Sweden, Austria and Germany between February 2007 and September 2011 to either four cycles of leukocyte nadir-based tailored and dose-dense adjuvant epirubicin (E) 38-120 mg/m 2, start at 90 mg/m 2) and cyclophosphamide (C) 450-1200 mg/m 2, start at 600 mg/m 2) Q2W, followed by four cycles of docetaxel (D) 75-100 mg/m 2, start at 75 mg/m 2) Q2W (three weeks pause between EC and D) (tdd arm) or three cycles of standard 5-Fluorouracil (F) 500 E100 C500 Q3W followed by three cycles of D100 Q3W (control arm). Total treatment duration was the same in the two arms. The primary endpoint was breast cancer relapse-free survival (BCRFS) assessed in the intention to treat population. Secondary endpoints included event-free surviva...

Host genotype and tumor phenotype of chemokine decoy receptors integrally affect breast cancer relapse.

Chemokines may play vital roles in breast cancer progression and metastasis. The primary members of chemokine decoy receptors (CDR), DARC and D6, are expressed in breast tumors and lymphatic/hematogenous vessels. CDRs sequestrate the pro-malignant chemokines. We hypothesized that breast cancer patients carrying different levels of CDR expression in tumor and/or in host might have differing clinical outcomes. This prospective observational study measured both expression and germline genotype of DARC and D6 in 463 primary breast cancer patients enrolled between 2004 and 2006. The endpoint was breast cancer relapse-free survival (RFS). There was a significant association between the co-expression of CDR (immunohistochemical expression of both DARC and D6) with RFS (hazard ratio [HR] of 0.32, 95% confidence interval [CI] 0.19 to 0.54). Furthermore, the co-genotype of two non-synonymous polymorphisms (with two major alleles of DARC-rs12075 and D6-rs2228468 versus the others) significantly related to relapse. Mechanistically, the variant-alleles of these two polymorphisms significantly decreased by 20-30% of CCL2/CCL5 (CDR ligands) levels relative to their major counterparts. Multivariate analysis highlighted that the co-expression and co-genotype of CDR were independent predictors of RFS, with HR of 0.46 (95% CI 0.27 to 0.80) and 0.56 (95% CI 0.37 to 0.85), respectively. The addition of host CDR genetic information to tumor-based factors (including co-expression of CDR) improved the relapse prediction ability (P = 0.02 of AUC comparison). The host genotype and tumor phenotype of CDR integrally affect breast cancer relapse. Host-related factors should be considered for individualized prediction of prognosis.

Abstract P5-10-02: A copy number aberration driven endocrine response gene signature stratifies risk in estrogen receptor positive breast cancer

Abstract Background: Many prognostic gene signatures have been developed for estrogen receptor positive (ER+) breast cancer (BC); however, most have been solely based on mRNA expression data without integrated information on underlying primary drivers such as genomic aberrations. We therefore coupled gene expression and copy number aberration (CNA) in an attempt to improve upon prognostic signatures for ER+ BC. Methods: mRNA expression based discovery was conducted between 172/59 ER+ BC with low/high Ki67 levels after neoadjuvant aromatase inhibition and significant genes (significance analysis of microarray, q-value less than 0.05) were screened by correlation (Mann-Whitney-Wilcoxon test P less than 0.05) with CNA using Agilent comparative genomic hybridization array. Further interrogation on prognosis of relapse-free survival (RFS) by univariate survival analysis (P less than 0.05) in patients treated with adjuvant endocrine monotherapy from a public data set produced a Copy Number Aberration Driven Endocrine Response (CADER) signature consisting of treatment sensitive/resistant genes. MetaCore (GeneGo Inc) pathway analysis was conducted for enriched pathways. We subsequently applied Nanostring nCounter technology to formalin fixed archival tumor RNA from 620 ER+ adjuvant tamoxifen treated BC (UBC TAM-series) for CADER gene profiling. Patients in multiple independent public data sets and the TAM-series were classified into treatment sensitive defined by up-regulated sensitive gene centroid and down-regulated resistant gene centroid by the median cutoffs, treatment resistant defined with the reverse pattern and indeterminate otherwise. CADER risk stratifications were associated with patient survival outcomes in public cohorts and the TAM-series. The Kaplan-Meier (KM) analysis and Cox models were used for survival analysis. Published PAM50 intrinsic subtypes and subtype based risk of relapse (ROR-S) assignments were used (Nielsen CCR 16:5222, 2010). Results: A 54-gene CADER signature, 27 resistant/27 sensitive genes, was derived. Pathway analysis indicated that CADER was enriched with sensitive genes of cell survival functions while resistant genes were largely drivers of cell cycle progression. CADER stratifications were significantly prognostic of relapse free survival (RFS) in all public cohorts (log rank test P=0.05 for all) and in the UBC TMA-series (P=0.0001, BC specific survival and RFS). CADER showed an additional value (likelihood ratio test P=0.05) in all cohorts when both standard clinical variables and ROR-S were incorporated in multivariate Cox models. CADER were highly concordant with intrinsic subtypes and ROR-S (p=0.0001) in all data sets. However, CADER may stratify risk within ROR-S medium risk patients (P=0.002 METABRIC; P=0.003 and 0.036 in TAM-series for BC specific survival and RFS). Conclusions: We have developed a signature that is prognostic of long-term survival in postmenopausal BC, further splits risk within ROR-S medium risk group and identifies some highly resistant BC in presence of ROR-S and clinical variables (see Ellis et. al. abstract for evaluation of a CADER single sample predictor in the MA12 Phase 3 clinical trial). Citation Format: Jingqin Luo, Li-Wei Chang, Yu Tao, Jeremy Hoog, Samuel Leung, Torsten O Nielsen, Matthew J Ellis. A copy number aberration driven endocrine response gene signature stratifies risk in estrogen receptor positive breast cancer [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P5-10-02.

PTIP Associated protein 1, PA1, Is an Independent Prognostic Factor for Lymphnode Negative Breast Cancer

Pax transactivation domain interacting protein (PTIP) associated protein 1, PA1, was a newly found protein participating in the modulation of transactivity of nuclear receptor super family members such as estrogen receptor (ER), androgen receptor (AR) and glucocorticoid receptor (GR). Breast cancer is one of the most life threatening diseases for women and has tight association with estrogen and ER. This study was performed to understand the function of PA1 in breast cancer. The expression of PA1 had been evaluated in a total of 344 primary invasive breast cancer samples and examined the relationship with clinical output, relapse free survival (RFS), breast cancer-specific survival (BCSS). PA1 expression was observed in both nucleus and cytoplasm, however, appeared mainly in nuclear. PA1 nuclear expression was correlated with postmenopausal (P = 0.0097), smaller tumor size (P = 0.0025), negative Ki67 (P = 0.02), positive AR (P = 0.049) and positive ERβ (P = 0.0020). Kaplan–Meier analysis demonstrated PA1 nuclear positive cases seemed to have a longer survival than negative ones for RFS (P = 0.023) but not for BCSS (P = 0.23). In the Cox hazards model, PA1 nuclear protein expression proved to be a significant prognostic univariate parameter for RFS (P = 0.03), but not for BCSS (P = 0.20). In addition, for those patients without lymphnode metastasis PA1 was found to be an independent prognostic factor for RFS (P = 0.025), which was verified by univariate and multivariate analyses. These investigations suggested PA1 expression could be a potential prognostic indicator for RFS in breast cancer.

Polycomb Protein EZH2 Regulates Tumor Invasion via the Transcriptional Repression of the Metastasis Suppressor RKIP in Breast and Prostate Cancer

Epigenetic modifications such as histone methylation play an important role in human cancer metastasis. Enhancer of zeste homolog 2 (EZH2), which encodes the histone methyltransferase component of the polycomb repressive complex 2 (PRC2), is overexpressed widely in breast and prostate cancers and epigenetically silences tumor suppressor genes. Expression levels of the novel tumor and metastasis suppressor Raf-1 kinase inhibitor protein (RKIP) have been shown to correlate negatively with those of EZH2 in breast and prostate cell lines as well as in clinical cancer tissues. Here, we show that the RKIP/EZH2 ratio significantly decreases with the severity of disease and is negatively associated with relapse-free survival in breast cancer. Using a combination of loss- and gain-of-function approaches, we found that EZH2 negatively regulated RKIP transcription through repression-associated histone modifications. Direct recruitment of EZH2 and suppressor of zeste 12 (Suz12) to the proximal E-boxes of the RKIP promoter was accompanied by H3-K27-me3 and H3-K9-me3 modifications. The repressing activity of EZH2 on RKIP expression was dependent on histone deacetylase promoter recruitment and was negatively regulated upstream by miR-101. Together, our findings indicate that EZH2 accelerates cancer cell invasion, in part, via RKIP inhibition. These data also implicate EZH2 in the regulation of RKIP transcription, suggesting a potential mechanism by which EZH2 promotes tumor progression and metastasis.

RNA structure: new messages in translation, replication and disease

The ‘Current Trends in Biomedicine’ workshop on the role of RNA structures in the translation of viral and cellular RNAs took place between 27 and 29 October 2008, in Baeza, Spain, and was organized by E. Martinez‐Salas, G. Belsham & J. Gomez. ![][1] See Glossary for abbreviations used in this article Since the elucidation of the genetic code approximately 40 years ago, the role of RNA in crucial biological processes has gained increasing attention, and is now one of the fastest developing areas in molecular biology and biochemistry. The advances made in structural studies of transfer RNA (tRNA), ribozymes, riboswitches, the ribosome and viral IRES elements in particular have shown the importance of secondary and tertiary structures in RNA biology, and have significantly changed our understanding of the translational control of gene expression (Fig 1). The World Heritage town of Baeza in Andalucia, Spain, hosted the ‘Current Trends in Biomedicine’ workshop on the role of RNA structures in the translation of viral and cellular RNAs. About 45 participants met in the beautiful buildings of the Sede Antonio Machado at the Universidad Internacional de Andalucia. Figure 1. Schematic illustration of discreet RNA regulatory elements. The translation of an mRNA is regulated by diverse mechanisms that involve both structural and non‐structural RNA elements, as well as interactions with RNA‐binding proteins. IRESes are found in the 5′ UTR and promote cap‐independent translation. Pseudoknots can be located in the 5′ UTR, the 3′ UTR, or the coding region, and their localization influences their effect on translation; for example, initiation, frameshifting and termination. 3′ UTR structural elements such as CREs, CITEs and SLs often function through long‐range RNA interactions. The miRNA target sites are located in the 3′ UTR. The canonical mRNA features of the cap (m7G) and poly(A) are targets of several regulatory interactions. The … [1]: /embed/graphic-1.gif

How Ki67 expression can predict relapse-free survival in breast cancer

How Ki67 expression can predict relapse-free survival in breast cancer

Molecular beacon reverse transcription-PCR of human chorionic gonadotropin-beta-3, -5, and -8 mRNAs has prognostic value in breast cancer.

The beta-subunit of human chorionic gonadotropin (hCG) is encoded by four genes, of which expression of the hCGbeta-3, -5, and -8 genes could have prognostic value in breast cancer. Applying a new, modified Molecular Beacon reverse transcription-PCR assay, we investigated the prognostic value of the hCGbeta-3, -5, and -8 gene transcripts in 129 sporadic unilateral breast cancer samples from patients with a median follow-up of 62.3 months. Expression of hCGbeta-3, -5, -8 was significantly (P = 0.020) associated with relapse-free survival (RFS). In multivariate survival analysis, hCGbeta-3, -5, and -8 maintained prognostic value for RFS, with high expression predicting shorter RFS (P = 0.015; hazard ratio, 2.25; 95% confidence interval, 1.17-4.34). Only 1 of 24 (4%) node-negative patients with low hCGbeta-3, -5, -8 expression relapsed, in contrast to 7 of 26 (27%) patients with high expression (P = 0.046). Expression of hCGbeta-3, -5, -8, which differ by only one nucleotide from other hCGbeta genes, can be assessed by our modified Molecular Beacon assay in breast cancer tissues. Expression of hCGbeta-3, -5, -8 has independent, prognostic value for RFS in breast cancer and may help identify node-negative patients with poor prognosis.